When you're using Reconstruction Mode, nothing changes in your city unless/until you save the changes you make. While you're doing it, in reality your buildings haven't moved yet, they're still sitting there as if you weren't doing anything. If you stop RM without saving any changes, it's as if you hadn't done anything. And if you save changes to your city, it instantly goes into the new configuration without skipping a beat. So there is no time in the process where any of your buildings/roads is not still actively in your city. At least, that's the way I understand the process.
